Add a utility to create a SSH tunnel for the database

gemma-core/src/main/java/ubic/gemma/persistence/util/LocalSshTunnel.java

@@ -0,0 +1,80 @@
+package ubic.gemma.persistence.util;
+
+import lombok.Setter;
+import lombok.extern.apachecommons.CommonsLog;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.ArrayUtils;
+import org.springframework.context.SmartLifecycle;
+import org.springframework.util.Assert;
+
+import javax.annotation.Nullable;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.concurrent.TimeUnit;
+
+/**
+ * Establishes a local SSH tunnel.
+ * @author poirigui
+ */
+@CommonsLog
+@Setter
+public class LocalSshTunnel implements SmartLifecycle {
+
+    private String host;
+    @Nullable
+    private Integer port;
+
+    // for the tunnel
+    private int localPort;
+    private String remoteHost;
+    private int remotePort;
+
+    private boolean autoStart = false;
+
+    private Process tunnelProcess;
+
+    @Override
+    public void start() {
+        Assert.isTrue( host != null && localPort > 0 && remoteHost != null && remotePort > 0 );
+        try {
+            String[] args = new String[] { "ssh", "-L", localPort + ":" + remoteHost + ":" + remotePort, host };
+            if ( port != null ) {
+                args = ArrayUtils.addAll( args, "-p", String.valueOf( port ) );
+            }
+            tunnelProcess = Runtime.getRuntime().exec( args );
+            // quickly check if the process exited
+            if ( tunnelProcess.waitFor( 100, TimeUnit.MILLISECONDS ) ) {
+                throw new RuntimeException( IOUtils.toString( tunnelProcess.getErrorStream(), StandardCharsets.UTF_8 ) );
+            }
+        } catch ( IOException | InterruptedException e ) {
+            throw new RuntimeException( e );
+        }
+        log.info( String.format( "Established a SSH tunnel to %s%s: %d -> %s:%d.",
+                host, port != null ? ":" + port : "", localPort, remoteHost, remotePort ) );
+    }
+
+    @Override
+    public void stop() {
+        tunnelProcess.destroy();
+    }
+
+    @Override
+    public boolean isRunning() {
+        return tunnelProcess != null && tunnelProcess.isAlive();
+    }
+
+    @Override
+    public boolean isAutoStartup() {
+        return autoStart;
+    }
+
+    @Override
+    public void stop( Runnable callback ) {
+        stop();
+    }
+
+    @Override
+    public int getPhase() {
+        return 0;
+    }
+}

gemma-core/src/main/resources/default.properties

@@ -50,6 +50,13 @@ gemma.db.user=gemmauser
 gemma.db.password=XXXXXX
 # Maximum size for the connections pool
 gemma.db.maximumPoolSize=10
+# Establish an SSH tunnel to connect to the database (only if the dev profile is active)
+gemma.db.tunnel.enabled=false
+gemma.db.tunnel.host=
+gemma.db.tunnel.port=
+gemma.db.tunnel.localPort=0
+gemma.db.tunnel.remoteHost=
+gemma.db.tunnel.remotePort=0
 ############################################################
 # SECURITY
 # Used to elevate authorities for some methods.
@@ -205,6 +212,13 @@ gemma.testdb.agent.userName=gemmaAgent
 gemma.testdb.agent.password=XXXXXXXX
 # Initialize the test database, this can be disabled to make integration tests faster
 gemma.testdb.initialize=true
+# Establish an SSH tunnel to connect to the test database (only if the dev profile is active)
+gemma.testdb.tunnel.enabled=false
+gemma.testdb.tunnel.host=
+gemma.testdb.tunnel.port=
+gemma.testdb.tunnel.localPort=0
+gemma.testdb.tunnel.remoteHost=
+gemma.testdb.tunnel.remotePort=0
 #the external database id to exclude by default in phenocarta
 gemma.neurocarta.exluded_database_id=85
 # Featured external databases in Gemma Web About page and Gemma REST main endpoint

gemma-core/src/main/resources/ubic/gemma/applicationContext-dataSource.xml

@@ -12,10 +12,35 @@
         <prop key="sessionVariables">sql_mode='STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION'</prop>
     </util:properties>
 
+    <beans profile="dev">
+        <bean id="tunnel" class="ubic.gemma.persistence.util.LocalSshTunnel">
+            <property name="host" value="${gemma.db.tunnel.host}"/>
+            <property name="port" value="${gemma.db.tunnel.port}"/>
+            <property name="localPort" value="${gemma.db.tunnel.localPort}"/>
+            <property name="remoteHost" value="${gemma.db.tunnel.remoteHost}"/>
+            <property name="remotePort" value="${gemma.db.tunnel.remotePort}"/>
+            <property name="autoStart" value="${gemma.db.tunnel.enabled}"/>
+        </bean>
+        <bean id="testTunnel" class="ubic.gemma.persistence.util.LocalSshTunnel">
+            <property name="host" value="${gemma.testdb.tunnel.host}"/>
+            <property name="port" value="${gemma.testdb.tunnel.port}"/>
+            <property name="localPort" value="${gemma.testdb.tunnel.localPort}"/>
+            <property name="remoteHost" value="${gemma.testdb.tunnel.remoteHost}"/>
+            <property name="remotePort" value="${gemma.testdb.tunnel.remotePort}"/>
+            <property name="autoStart" value="${gemma.testdb.tunnel.enabled}"/>
+        </bean>
+    </beans>
+
+    <beans profile="!dev">
+        <!-- placeholders to satisfy depends-on -->
+        <bean id="tunnel" class="java.lang.Object"/>
+        <bean id="testTunnel" class="java.lang.Object"/>
+    </beans>
+
     <!-- we use the same database for production and development -->
     <beans profile="production,dev">
         <!-- Database connection information -->
-        <bean id="dataSource" class="com.zaxxer.hikari.HikariDataSource" destroy-method="close">
+        <bean id="dataSource" class="com.zaxxer.hikari.HikariDataSource" destroy-method="close" depends-on="tunnel">
             <property name="poolName" value="gemma"/>
             <property name="driverClassName" value="com.mysql.cj.jdbc.Driver"/>
             <property name="username" value="${gemma.db.user}"/>
@@ -36,7 +61,7 @@
     </beans>
 
     <beans profile="test,testdb">
-        <bean id="dataSource" class="com.zaxxer.hikari.HikariDataSource" destroy-method="close">
+        <bean id="dataSource" class="com.zaxxer.hikari.HikariDataSource" destroy-method="close" depends-on="testTunnel">
             <property name="driverClassName" value="com.mysql.cj.jdbc.Driver"/>
             <property name="username" value="${gemma.testdb.user}"/>
             <property name="password" value="${gemma.testdb.password}"/>